The slow things tend to be the sort of numerical loops that you see in micro-benchmarks. It's no coincidence that the version of Python in the linked article saw its greatest speed up in a numerical loop, but only modest improvement elsewhere. It's exactly this sort of simple repetitive operation where interpreter overhead matters the most.
Language features that encapsulate complex functionality tend to be harder to speed up in CPython because the VM operates at a fairly high level. In effect you're just kicking off a large subroutine that is written in C, and you're really executing native code until that operation is complete. You're not going to improve very much on that no matter how much you try.
What this means is that speed will depend heavily on the type of application program being written, and also on how much the programmer takes advantage of the unique language features. It also makes realistic cross language benchmarks difficult because the right way to do something in Python may not have a direct equivalent in another language. The result tends to be "lowest common denominator" benchmarks, which are exactly the sort of algorithms which CPython does worst at.